[Biopython-dev] Subclassing Seq objects from a string

[Peter Cock]

True doing the subclassing would immediately define the missing methods by
default, but then risk a behavior change later as we make them sequence
aware. Please try this on a branch or pull request?

Peter


On Wed, Jun 28, 2017 at 11:20 AM, Michiel de Hoon <mjldehoon at yahoo.com>
wrote:

> We could move faster by doing the subclassing first. There is a price for
> being too rigorous: Improvements are taking too long to happen. Ten years
> in this case.
>
> Best,
> -Michiel
>
>
> On Monday, June 26, 2017 6:21 PM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>
>
> Hello all,
>
> Looking at the mailing list archive, the plain text version didn't capture
> Michael's link to the thread ten years ago:
>
> http://lists.open-bio.org/pipermail/biopython/2007-August/009867.html
>
> We're still at step two of that outlined plan:
>
> Peter wrote in August 2007:
> > (1) Modify Seq .__str__() method to ... return self.data
> >
>
> Done, along with changes to __eq__ to match etc.
>
> > (2) Consider adding alphabet aware versions selected string methods to
> > the Seq object (e.g. count, find)
>
> While we have count, find, upper, lower, etc we still don't have all the
> string methods defined for the Seq object (e.g. replace is missing -
> what else?)
>
> > Then, for the release afterwards:
> > (3) actually do the class inheritance with all the horrors entailed.
>
> And this is of course pending - as per this thread title.
>
> --
>
> Note that in addition to supporting all the base string methods, we
> still want the Seq object to also support extra biological methods
> and perhaps additional optional arguments, e.g. overlapping counts:
>
> https://github.com/biopython/biopython/issues/1294
>
> Other than the translate method (mentioned below), I don't think we
> have any name or argument clashes to worry about.
>
> Regards,
>
> Peter
>
>
> On Wed, May 24, 2017 at 10:28 AM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
> >
> > Hi Michiel,
> >
> > I think we'd need to work on making the API more string like before it
> would be practical to considering subclassing.
> >
> > Would anyone like to make a list of all the string methods which we do
> not currently implement, starting with replace (where dealing with the
> alphabet is tricky if new letters are introduced)?
> >
> > Then there is the translate method where we deliberately did not follow
> the Python string method behaviour, but it would be possible to match it as
> a special case where currently we issue an exception:
> >
> > https://github.com/biopython/biopython/blob/biopython-169/
> Bio/Seq.py#L985
> >
> > Peter
> >
> >
> >
> >
> > On Tue, May 23, 2017 at 2:32 AM, Michiel de Hoon <mjldehoon at yahoo.com>
> wrote:
> >>
> >> Dear all,
> >>
> >> Ten years ago we talked about subclassing Seq objects from a string:
> >>
> >> [BioPython] Making the Seq object act more like a string
> >> http://lists.open-bio.org/pipermail/biopython/2007-August/009867.html
>
> >>
> >> Can we move forward?
> >> As the Seq documentation says, a Seq object is essentially a string
> with an alphabet.
> >> Then, following the object oriented programming paradigm, Seq objects
> should inherit from a string object.
> >>
> >> This would help with C extensions that take Seq or string objects as
> arguments (as both can then be treated as strings).
> >>
> >> Best,
> >> -Michiel
> >>
> >> _______________________________________________
> >> Biopython-dev mailing list
> >> Biopython-dev at mailman.open-bio.org
> >> http://mailman.open-bio.org/mailman/listinfo/biopython-dev
> >
> >
>
>
>
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